Radio Frequency (RF) signals transmitted by Global Navigation Satellite Systems (GNSS) are exploited as signals of opportunity in many scientific activities, ranging from sensing waterways and humidity of the terrain to the monitoring of the ionosphere. The latter can be pursued by processing the GNSS signals through dedicated ground-based monitoring equipment, such as the GNSS Ionospheric Scintillation and Total Electron Content Monitoring (GISTM) receivers. Nonetheless, GNSS signals are susceptible to intentional or unintentional RF interferences (RFIs), which may alter the calculation of the scintillation indices, thus compromising the quality of the scientific data and the reliability of the derived space weather monitoring products. Upon the observation of anomalous scintillation indices computed by a GISTM receiver in the Mediterranean area, the study presents the results of the analysis and characterization of a deliberate, unclassified interferer acting on the L1/E1 GNSS signal bands, observed and captured through an experimental, software defined radio setup. The paper also highlights the adverse impacts of the interferer on the amplitude scintillation indices employed in scientific investigations, and presents a methodology to discriminate among regular and corrupted scintillation data. To support further investigations, a dataset of baseband signals samples affected by the RFI is available at IEEE DataPort.